The debate between Neelix and Jetrel resembles the debate that took place before the bomb was dropped on Hiroshima. It was discussed dropping it in an uninhabited area to demonstrate its power, but it was ultimately decided that wouldn't be a powerful enough message so Hiroshima was chosen.
The writers of this episode focused it around a character, Jetrel, whom they based on J. Robert Oppenheimer, using him as a basis to shed light on the persona of Neelix. In fact, Kenneth Biller once described the installment as "Neelix meets Robert Oppenheimer."
Actor James Sloyan says the phrase "What I did had to be done" as both Jetrel in this episode, and as Admiral Jarok in The Defector (1990).
The episode was a conscious attempt to recreate the chemistry and powerful dramatic effect of Duet (1993). (Both episodes were the penultimate in the first season of their respective shows.) Whereas "Duet" was an allegory for the Nazi German treatment of several communities, this episode was a metaphor for the aftermath of the United States' nuclear bombing of Nagasaki and Hiroshima during World War II.